Structure of PDB 6p5k Chain AI

Receptor sequence

>6p5kAI (length=205) Species: 9986 (Oryctolagus cuniculus)

GRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGH
MVSDEYEQLSSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINK
MLQTGMRGAFGKPQGTVARVHIGQVIMSIRTKLQNKEHVVEALRRAKFKF
PGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGPLDKW
RALHS

3D structure

• PDB: 6p5k The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs.
• Chain: AI
• Resolution: 3.1 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	AI	R3 R4 A6 R7 C8 Y9 K15 P16 Y17 F22 R24 D35 K39 K40 S61 E63 A64 A67 K74 R88 R90 H92 F94 R98 N100 G114 M115 R116 G117 A118 F119 G120 Q133 F157 K158 P160 R162 K175 D193 G194 C195	R2 R3 A5 R6 C7 Y8 K14 P15 Y16 F21 R23 D34 K38 K39 S60 E62 A63 A66 K73 R87 R89 H91 F93 R97 N99 G105 M106 R107 G108 A109 F110 G111 Q124 F148 K149 P151 R153 K166 D184 G185 C186
BS02	rna	AI	Y11 E56 Y57 I131 Y199 N202 R203 G204 P205 L206 W209	Y10 E55 Y56 I122 Y190 N193 R194 G195 P196 L197 W200
BS03	rna	AI	R32 I33	R31 I32

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation
• GO:0006417 regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6p5k, PDBe:6p5k, PDBj:6p5k
• PDBsum: 6p5k
• PubMed: 31609474
• UniProt: B7NZQ2|RL10_RABIT Large ribosomal subunit protein uL16 (Gene Name=RPL10)